In a deliberate attempt to block a shot, kimpembe placed himself in a way that a certain part of his body (his right arm) with which you can not attempt to play the ball gave him an unfair advantage. Thus, this part of the body was in an unnatural position in football terms.
Skomina took more time trying to calm down the two benches than reviewing the incident for crying out loud. I think he saw it only twice and he immediately made up his mind. It was that easy. Ex-players, especially defenders like Rio, will always believe that the defender should be given more slack in situations such as this one. As for Michael "i would instruct my lads to finish off an injured player" Owen, i don't give a flying rat's arse about what he thinks.
The problem stems from the inconsistency among referees in such situations and from the (quite reasonable tbf) belief among many football fans that because of the fact that a penalty call gives to one of the two teams the clearest of goal-scoring opportunities, it should be awarded only when such an opportunity has been denied by the defender in open play. But this is not the case according to the laws of the game which state that a penalty is simply a foul inside the box. If it had been outside the box, nobody would be talking about it. And if Kimpmmbe had been on the goal-line and his arm had been the only thing preventing the ball from hitting the net, nobody would be talking about it either. And nobody should be talking about it now, because according to the laws of the game the ref made the right call.
And the right call isn't necessarily a popular one. Despite what all the world (me included), except for the Real Madrid fans, wanted, Oliver made the right call at the Bernabeu last season. Similarly, if Southampton had been awarded two penalties last Saturday (with VAR in effect they would probably have got at least one), we would have nothing to complain about. There's not a single defender who will admit that he placed his body in a way that would make his body bigger and, as ex-referees in my country like to say, "there's no dynamometer available to check whether the attacker was pushed or if he went down easily, so the defender should be very careful with how he uses his hands". In the end, Kimpembe with his skating axel gave Skomina a decision to make and VAR is there to help refs enforce the letter of the law (with slow replays, different angles etc., that's where it's heading to). After that, i'll let you do the math.